rs1547531

Variant names:

• chr5-30796284-G-A
• rs1547531
• ENST00000797583.1:n.369-5625C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000797583.1(ENSG00000303861):​n.369-5625C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 151,926 control chromosomes in the GnomAD database, including 49,900 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.81 (49900 hom., cov: 31)
• Consequence: ENSG00000303861 ENST00000797583.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 2 publications found

Genes affected

ENSG00000303861 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303861	ENST00000797583.1	n.369-5625C>T		intron_variant	Intron 4 of 4
ENSG00000303861	ENST00000797584.1	n.277-5625C>T		intron_variant	Intron 1 of 2
ENSG00000303861	ENST00000797585.1	n.184-5625C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122660 AN: 151810 Hom.: 49848 Cov.: 31

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.806

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.808 AC: 122771 AN: 151926 Hom.: 49900 Cov.: 31 AF XY: 0.809 AC XY: 60100 AN XY: 74246

African (AFR) AF: 0.868 AC: 36020 AN: 41488

American (AMR) AF: 0.821 AC: 12498 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2666 AN: 3466

East Asian (EAS) AF: 0.968 AC: 4978 AN: 5140

South Asian (SAS) AF: 0.879 AC: 4236 AN: 4818

European-Finnish (FIN) AF: 0.712 AC: 7513 AN: 10550

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52275 AN: 67928

Other (OTH) AF: 0.807 AC: 1701 AN: 2108

Alfa AF: 0.782 Hom.: 24022

Bravo AF: 0.820

Asia WGS AF: 0.913 AC: 3173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.69
DANN	Benign	0.47
PhyloP100		-0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1547531; hg19: chr5-30796391;